SMTL ID : 7p87.1 (1 other biounit)

Crystal structure of YTHDC1 with compound YLI_DC1_001

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x ID0: N-methyl-4,5,6,7-tetrahydro-1H-indazole-3-carboxamide(Non-covalent)

ID0.1: 10 residues within 4Å: Chain A: N.37, N.41, W.51, S.52, T.53, L.54, W.102, P.105, M.108, D.150 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.54, A:P.105 Hydrogen bonds: A:N.41, A:S.52, A:D.150 Water bridges: A:N.37

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.18, A:S.20, A:K.21 Water bridges: A:T.19, A:S.20, A:S.20, A:K.21, A:K.21, A:L.22 Salt bridges: A:K.21 SO4.3: 2 residues within 4Å: Chain A: R.149, D.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:D.150 SO4.4: 2 residues within 4Å: Chain A: H.94, H.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.95 Water bridges: A:S.93 Salt bridges: A:H.94, A:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structure-based design of ligands of the m6A-RNA reader YTHDC1. Eur J Med Chem Rep (2022)

Release Date

2021-10-20

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing protein 1

Related Entries With Identical Sequence